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Calcium in PDB 3m36: Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423):
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423), PDB code: 3m36 was solved by R.S.Alexander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.74 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.800, 72.300, 77.700, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.4

Other elements in 3m36:

The structure of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) (pdb code 3m36). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423), PDB code: 3m36:

Calcium binding site 1 out of 1 in 3m36

Go back to Calcium Binding Sites List in 3m36
Calcium binding site 1 out of 1 in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:66.9
occ:1.00
 OE2 A:GLU77 2.9 39.7 1.0
OD2 A:ASP70 3.0 30.9 1.0
O A:GLN75 3.1 56.1 1.0
OD1 A:ASP70 3.1 31.2 1.0
O A:ASN72 3.2 32.9 1.0
CG A:ASP70 3.3 31.0 1.0
O A:HOH490 3.4 49.5 1.0
CG A:GLU80 3.6 36.4 1.0
OE1 A:GLU76 3.8 64.3 1.0
CD A:GLU80 3.9 39.5 1.0
OE1 A:GLU80 4.0 37.8 1.0
CA A:THR73 4.0 40.1 1.0
O A:THR73 4.0 42.6 1.0
C A:THR73 4.1 42.4 1.0
CD A:GLU77 4.1 45.8 1.0
C A:ASN72 4.1 34.1 1.0
C A:GLN75 4.2 56.9 1.0
NH1 A:ARG67 4.2 31.2 1.0
CA A:GLU76 4.3 57.6 1.0
N A:THR73 4.5 36.5 1.0
OE2 A:GLU80 4.6 44.4 1.0
CB A:ASP70 4.6 28.5 1.0
CZ A:ARG67 4.6 30.7 1.0
O A:GLU74 4.7 52.7 1.0
N A:GLU76 4.7 57.5 1.0
CB A:GLU80 4.7 35.1 1.0
C A:GLU76 4.7 56.5 1.0
CD A:ARG67 4.8 28.2 1.0
N A:GLU74 4.8 45.3 1.0
NE A:ARG67 4.9 30.8 1.0
CG A:GLU77 4.9 47.0 1.0
OE1 A:GLU77 4.9 41.4 1.0
C A:GLU74 4.9 51.8 1.0
CD A:GLU76 5.0 63.8 1.0

Reference:

J.R.Pruitt, D.J.P.Pinto, R.A.Jr.Galemmo, R.S.Alexander, K.A.Rossi, B.L.Wells, S.Drummond, L.L.Bostrom, D.Burdick, R.Bruckner, H.Chen, A.Smallwood, P.C.Wong, M.R.Wright, S.Bai, J.M.Luettgen, R.M.Knabb, P.Y.S.Lam, R.R.Wexler. Discovery of 1-(2-Aminomethylphenyl)-3-Trifluoromethyl-N-[3- Fluoro-2'-(Aminosulfonyl)[1,1'-Biphenyl)]-1H- Pyrazole-5-Carboxyamide (DPC602), A Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor J.Med.Chem. V. 46 5298 2003.
ISSN: ISSN 0022-2623
PubMed: 14640539
Page generated: Tue Jul 8 14:29:08 2025

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